Antisense oligonucleotides are small oligonucleotides which are complementary to the "sense" or coding strand of a given gene, and as a result are also complementary to, and thus able to specifically hybridize with, the mRNA transcript of the gene. For an antisense oligonucleotide to be effective, the complementary target sequence must be available for hybridization. However, the RNA target is not a single stranded random coil but contains secondary and tertiary structures. Target RNA structure has been shown to affect affinity and rates of oligonucleotide hybridization (Freier, S. M. & Tinoco, I. Jr., Biochemistry 14 1975 3310. Uhlenbeck, O. C., J. Mol. Biol. 65 1972, 25. Yoon, K., Turner, D. H., & Tinoco, I. Jr., J. Mol. Biol. 99 1975, 507. Fedor, M. J. & Uhlenbeck, O. C., Proc. Natl. Acad. Sci. USA 87 1990, 1668. Herschlag, D. & Cech, T. R., Biochemistry 29 1990a, 10159. Herschlag, D. & Cech, T. R., Biochemistry 29 1990b, 10172) as well as efficacy of antisense oligonucleotides (Bacon, T. A. & Wickstrom, E., Oncogene Res. 6 1991, 13. Wickstrom, E., Simonet, W. S., Medlock, K., & Ruiz-Robles, I., Biophys. J. 49 1986, 15. Chiang, M. -Y., Chan, H., Zounes, M. A., Freier, S. M., Lima, W. F., & Bennett, C. F., J. Biol. Chem. 266 1991, 18162). However, there is a need for a method for preparing antisense oligonucleotides which takes advantage of target secondary and tertiary structure in the preparation of effective oligonucleotides.